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Cancer Epidemiol Biomarkers Prev. 2017 Jan;26(1):126-135. doi: 10.1158/1055-9965.EPI-16-0106. Epub 2016 Oct 3.

The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers.

Author information

1
Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire. Christopher.I.Amos@dartmouth.edu.
2
Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom.
3
Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
4
Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire.
5
Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, Ohio.
6
The Center for Bioinformatics and Functional Genomics at Cedars Sinai Medical Center, Greater Los Angeles Area, Los Angeles, California.
7
Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California.
8
Department of Epidemiology, Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts.
9
Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
10
Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland.
11
Molecular Cancer Epidemiology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.
12
Van Andel Research Institute, Grand Rapids, Michigan.
13
Cedars-Sinai Medical Center, Los Angeles, California.
14
Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark.
15
Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland.
16
Génome Québec Innovation Centre, Montreal, Canada and McGill University, Montreal, Canada.
17
University Health Network- The Princess Margaret Cancer Centre, Toronto, California.
18
Huntsman Cancer Institute, Salt Lake City, Utah.
19
Mayo Clinic, Rochester, Minnesota.
20
Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia.
21
Cancer, Genetics and Immunology, Menzies Institute for Medical Research, Hobart, Australia.
22
Division of Biostatistics, Department of Preventive Medicine, Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California.
23
Department of Genetic Epidemiology, University Medical Center, Georg-August-University, Göttingen, Germany.
24
University of Salzburg and Cancer Cluster Salzburg, Salzburg, Austria.
25
Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg, Germany.
26
Translational Lung Research Center Heidelberg, Member of the German Center for Lung Research, Heidelberg, Germany.
27
Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
28
Helmholtz Zentrum München, Institut für Epidemiologie I, Neuherberg, Oberschleissheim, Germany.
29
Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland.
30
Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec and Laval University, Québec City, Canada.
31
Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany.
32
Institute of Cancer Research, London, England.
33
Department of Epidemiology, University of Washington, Seattle, Washington.
34
International Agency for Research on Cancer, World Health Organization, Lyon, France.
35
Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina.
36
Department of Gynecology, Duke University Medical Center, Durham, North Carolina.
37
Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
38
Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, P.R. China.
39
Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, P.R. China.
40
Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark.
41
Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center, Tampa, Florida.
42
Molecular and Genetic Epidemiology Group, National Institute for Environmental Health Sciences, Research Triangle Park, North Carolina.
43
Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom.
44
College of Medicine, Seoul National University, Gwanak-gu, Seoul, Korea.
45
Clinical Genetics Service, Memorial Hospital, New York, New York.
46
Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, New York.
47
Department of Medicine, Weill Cornell Medical College, New York, New York.
48
Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.
49
Zentrum Familiärer Brust- und Eierstockkrebs, Universitätsklinikum Köln, Köln, Germany.
50
Department of Molecular Medicine, Sapienza, University of Rome, Rome, Italy.
51
Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, University of Toronto, Toronto, Canada.
52
Department of Statistics, Oxford University, Oxford, United Kingdom.
53
Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.
54
Department of Biochemistry and Molecular Medicine, University of California at Davis, Davis, California.
55
Department of Internal Medicine, University of California at Davis, Davis, California.
56
Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland.

Abstract

BACKGROUND:

Common cancers develop through a multistep process often including inherited susceptibility. Collaboration among multiple institutions, and funding from multiple sources, has allowed the development of an inexpensive genotyping microarray, the OncoArray. The array includes a genome-wide backbone, comprising 230,000 SNPs tagging most common genetic variants, together with dense mapping of known susceptibility regions, rare variants from sequencing experiments, pharmacogenetic markers, and cancer-related traits.

METHODS:

The OncoArray can be genotyped using a novel technology developed by Illumina to facilitate efficient genotyping. The consortium developed standard approaches for selecting SNPs for study, for quality control of markers, and for ancestry analysis. The array was genotyped at selected sites and with prespecified replicate samples to permit evaluation of genotyping accuracy among centers and by ethnic background.

RESULTS:

The OncoArray consortium genotyped 447,705 samples. A total of 494,763 SNPs passed quality control steps with a sample success rate of 97% of the samples. Participating sites performed ancestry analysis using a common set of markers and a scoring algorithm based on principal components analysis.

CONCLUSIONS:

Results from these analyses will enable researchers to identify new susceptibility loci, perform fine-mapping of new or known loci associated with either single or multiple cancers, assess the degree of overlap in cancer causation and pleiotropic effects of loci that have been identified for disease-specific risk, and jointly model genetic, environmental, and lifestyle-related exposures.

IMPACT:

Ongoing analyses will shed light on etiology and risk assessment for many types of cancer. Cancer Epidemiol Biomarkers Prev; 26(1); 126-35. ©2016 AACR.

PMID:
27697780
PMCID:
PMC5224974
DOI:
10.1158/1055-9965.EPI-16-0106
[Indexed for MEDLINE]
Free PMC Article

Conflict of interest statement

There are no conflicts of interest

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